Dregg makes a proposition to any warrior that they will be showered with wealth and power if they can last 90 seconds against the Turtles. The Turtles seem to be a match for the aliens fueled by Dregg's motivation that keep appearing in their dimension.

Dregg, now clearly insane, has tricked the alien warriors and absorbs all of their strength. He is now able to overpower the Turtles. Donatello has an idea to use the portal to recover Krang's old android body. This will be the Turtles' only weapon to shut down the maniacal alien once and for all.moreless

Dregg launches a vicious attack on New York City. Though again unable to defeat the Turtles, the harm is done. Worse, he and Mung embark on more dangerous ideas. With the newly modified Dreggnaut transporter, Earth can be sent into Dimension X. When the portal appears, the Turtles, Splinter and April quickly see what is going on. Time is not on their side, however. With April staying behind at the lair, the Turtles and Splinter quickly race into action. Unfortunately, a mix-up separates them. Only Splinter makes it to the Dreggnaut, while the Turtles find themselves in different, strange locations. Fighting against major odds, he also works to reunite his sons and get them to the Dreggnaut. He succeeds and the Turtles are soon facing Dregg again. The five turn Dregg's own plan against him and make it back home, while their foe is once again defeated.moreless

The community gets a first look at the amazing Protein Computer, including the secretly-in-attendance Turtles. A brain link can easily grant one control of any piece of technology – making the possibilities endless. A need for action arises, however, as gangsters want to kidnap inventor Professor Alvin Huxley and steal the Protein Computer. Though the Turtles defeat them, the danger is far from over. As ordinary as the gangsters are, their boss – the interdimensional Globfather – sure isn't. He stands to collect a hefty reward from Dregg in exchange for Huxley's invention. He sends the gangsters out again to do the job right this time. Despite the Turtles' best efforts, they get Professor Huxley, but his son gets away and unknowingly with the Protein Computer. Both sides search for Ronnie, but the Globfather wins out. Now, the Turtles race to stop the Globfather and then Dregg from wreaking havoc on Earth. They succeed, but this victory may be short-lived in the long run.moreless

While both groups of the Turtles are trying to survive from Dregg's attack, Dregg moves forward with his attack plan. Shredder and Krang won't be defeated so easily, and complicate things for Dregg. While Dregg holds off Shredder and the Turtles, he demands total control of all governments from the United Nations or the Earth will get a little crispy. Also, Carter must cure his mutation, along fighting with the Turtles.moreless

The Turtles, Shredder and Krang's battles skills, powers, and memories are absorbed into Dregg, and he becomes a super-being. He detains his drained prisoners and prepares to initiate the final stage of his plan to conquer earth by using the matter transporters to project pieces of the very sun itself onto any city of his choosing, he will continue to do so until Earth conveys onto him the title of emperor.

Splinter, meanwhile, is visited by time-travellers from the distant future, which has come to aid the TMNT, at the approval of Splinter, they travel back two years, and pluck a team of turtles from the past. But there is a price to pay for this deed, the past Turtles only have 24 hours before they must be sent back, or the turtle's present timeline will cease to exist.

The past TMNT, together with Carter arrive on board the Dreggnaught, and after a fierce battle with Dregg's underlings, are able to rescue the present-day TMNT, but their skills and experience are still retained by Dregg. The Turtles use the transporters to return to earth, only to find Dregg's doomsday machines waiting for them when they arrive at the warehouse.

Aboard the Dreggnaught, Dregg and Mung are discussing their next move against the Turtles when Mung informs Dregg that, whilst scouting dimensions, he came across two individuals who claimed they were "old acquaintances of the turtles": Shredder and Krang!

Intrigued by the prospect of using the TMNT's mortal enemies as pawns in his grand scheme, Dregg makes preparations to bring Shredder and Krang back to earth. Meanwhile, Donatello cures Carter of his mutation disease, using the process he used to cure his brothers. Carter, wanting to return to civilization decides the time has come to leave The TMNT and New York behind him, and says goodbye.

Elsewhere, at the power plant, Dregg and Mung activate the Vortex Transporter, which causes a citywide blackout, but in Dregg's eyes, the chaos is all worth the effort, as the transporter succeeds in bringing Shredder and Krang back. But the two villains prove to be as sly as Dregg when they are able to get away from him, proclaiming that they and they alone will dominate the earth. They flee into the city.

Carter, meanwhile, sees the chaos that has gripped the city since the blackout, after saving a cab filled with civilians, he changes his mind about leaving.

The blackout has also caused traffic to grind to a halt, and April isn't happy about it, she thinks things can't get any worse, and then Shredder and Krang hijack her cab, and promptly kidnap her. April is able to contact the Turtles, but Shredder cuts her off, they soon find her cab, but it's empty, Krang and Shredder have decided to proceed on foot.

Mungg is able to locate both the TMNT and their foes and transports all of them back to the Power Plant, where Dregg is preparing to subject them to his greatest, most insidious experiment, Shredder tricks Dregg into thinking he's changed his mind about working with him in conquering earth, and the deception pays off, Shredder and Krang engage in a gun-battle with Dregg's soldiers, the Turtles join in the conflict also, and soon all three parties are fighting one another.

But Dregg uses his micro-bots to turn the tide, and recaptures his foes. He then reveals what he intends to do with them: drain their mental energies and infuse them into his own body, with Shredder and the TMNT's honed battle skills and Krang's superior intelligence, Dregg will become the most omnipotent being in this or any other galaxy!

Having recaptured the mutated Leonardo, the Turtles quickly restore him to normal using the vortex crystal technology. At first, it seems that the experiment has worked this time, but soon Leonardo's foot starts glowing, he still has the disease, and which means it's only a matter of time until he mutates once more...

Dregg commands Mung to take control of a power plant so he can commandeer it's vast supply of plutonium. April, still itching to sink her teeth into a new story, investigates a chop-chop ring at work in the city. Leonardo completely mutates again, and the TMNT once again are thrown into a heated to coral their slightly-more-mutated-than-usual-leader, which takes them across the city and back. The TMNT'S pursuit of Leonardo is interrupted by Dregg, who captures him. Meanwhile, April's investigation of the chop-chop ring leads her right into the arms of dregg's soilders... AGAIN.

On board the Dreggnaught, Dregg informs the turtles, (who had stowed away on the vessel after Dregg captured their leader, only to be captured), informs the turtles that his new vortex crystal-powered generator, will take out the unstable mutated cells in Leonardo's DNA, giving Dregg unlimited access to study and harness the power of the disease to his own ends! After Dregg cures Leonardo with the generator, the Turtles are able to escape and battle Dregg's minions. They rescue April and Leonardo and flee the Dreggnaught, at the same time they prevent Dregg from using the cells to cause further havoc. As the TMNT celebrate the end of their mutation nightmare, their prowess is monitored by Dregg, who informs Mung that he permanently altered Leonardo's DNA structure, and soon he may just put such an alteration to his advantage...moreless

The Turtles are working on once and for all ridding themeselves of thier mutations, Donatello makes use of a Virtual Reality Programm to test out the effects of a potential cure he has created using the Vortex Crystals. On his homeworld, Dregg schemes to return to Earth, his chief scientist, Mung presents the micro-bots capable of creating advanced machinery in seconds rather than days or months, as well as track down the Vortex Crystals presently being used on earth.

Back on earth, Donatello tries out his cure on both himself and the rest of the TMNT for real. It works, well, at least on MOST of the green machine, one of the micro-bots Dregg sent to Earth to find the vortex crystals, has located the source at the lair. Unseen, it steals one of the crystals just as Leonardo receives treatment for his own mutation. The experiment goes without a hitch, and Leonardo seems fine until later, when he suddenly mutates and goes on a rampage across New York.

April, Investigating a recent power outage at the Hydroelectric dam, stumbles onto Dregg (having arrived on Earth VIA his ship the Dreggnaught) and discovers he is using the Microbots to create a dimensional transporter, she contacts the Turtles, but she is caught by Dregg. After a dramatic chase, The TMNT are able to capture Leonardo, and they set out to rescue April, in the ensuing battle, the Turtles are tricked and captured by Dregg.

Before the TMNT can be used as guinea pigs in Dregg's dimesional transporter, the mutated Leonardo bursts out of the Turtle Van and tears the place apart. Dregg and Mungg escape in the Transporter before it explodes, and the TMNT escape the factory as it collapses completly, but although April, and the day, has been saved, Leonardo is still mutated, and Dregg is still at large...

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